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State Embedding model checkpoints are meant to be used with the [Arc State](https://pypi.org/project/arc-state/) repository.
State is distributed via [`uv`](https://docs.astral.sh/uv).
## Running from pypi
```bash
uv tool install arc-state
```
To generate embeddings given an AnnData:
```code
state emb --model-folder <SE-600M_MODEL_PATH> --input <INPUT_ANNDATA>.h5ad --output <OUTPUT_PATH>.h5ad
```
## Running from source
```bash
# Clone repo
git clone github.com:arcinstitute/state
cd state
# Initialize venv
uv venv
# Install
uv tool install -e .
```
To generate embeddings given an AnnData:
```code
state emb --model-folder <SE-600M_MODEL_PATH> --input <INPUT_ANNDATA>.h5ad --output <OUTPUT_PATH>.h5ad
```
For model licenses please see `MODEL_ACCEPTABLE_USE_POLICY.md`, `MODEL_LICENSE.md`, and `LICENSE.md`. |